FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
Ps2Ex3M1_Heter_6month_07_07_2016_F3_80_FemAligned.sortedByCoord.out.bam 87,396,876 0 8-150 51
Ps2Ex3M1_Heter_6month_07_07_2016_F3_81_FemAligned.sortedByCoord.out.bam 86,458,883 0 3-150 51
Ps2Ex3M1_Heter_6month_07_07_2016_F3_84_FemAligned.sortedByCoord.out.bam 98,729,835 0 2-150 57
Ps2Ex3M1_Heter_6month_07_07_2016_F3_89_FemAligned.sortedByCoord.out.bam 91,119,306 0 8-150 50
Ps2Ex3M1_Hom_6month_07_07_2016_F3_78_FemAligned.sortedByCoord.out.bam 86,141,677 0 8-150 50
Ps2Ex3M1_Hom_6month_07_07_2016_F3_82_FemAligned.sortedByCoord.out.bam 74,106,252 0 3-150 50
Ps2Ex3M1_Hom_6month_07_07_2016_F3_83_FemAligned.sortedByCoord.out.bam 81,899,755 0 6-150 51
Ps2Ex3M1_Hom_6month_07_07_2016_F3_85_FemAligned.sortedByCoord.out.bam 85,231,920 0 8-150 51
Ps2Ex3M1_WT_6month_07_07_2016_F3_79_FemAligned.sortedByCoord.out.bam 61,896,154 0 5-150 49
Ps2Ex3M1_WT_6month_07_07_2016_F3_86_FemAligned.sortedByCoord.out.bam 66,240,830 0 8-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_88_FemAligned.sortedByCoord.out.bam 82,993,606 0 8-150 51
Ps2Ex3M1_WT_6month_07_07_2016_F3_95_FemAligned.sortedByCoord.out.bam 70,719,422 0 2-150 48

Read Totals

Library Sizes ranged between 61,896,154 and 98,729,835 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Drerio Genome

GC Content Distributions for all reads showing theoretical GC content from the Drerio Genome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from Ps2Ex3M1_Heter_6month_07_07_2016_F3_80_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Heter_6month_07_07_2016_F3_81_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Heter_6month_07_07_2016_F3_84_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Heter_6month_07_07_2016_F3_89_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Hom_6month_07_07_2016_F3_78_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Hom_6month_07_07_2016_F3_82_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Hom_6month_07_07_2016_F3_83_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_Hom_6month_07_07_2016_F3_85_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_WT_6month_07_07_2016_F3_79_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_WT_6month_07_07_2016_F3_86_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_WT_6month_07_07_2016_F3_88_FemAligned.sortedByCoord.out.bam
## Overrepresented_sequences missing from Ps2Ex3M1_WT_6month_07_07_2016_F3_95_FemAligned.sortedByCoord.out.bam
## No overrepresented sequences were detected by FastQC

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.1.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.3), ngsReports(v.1.1.4), tibble(v.2.1.3), ggplot2(v.3.2.1) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.55.0), lubridate(v.1.7.4), webshot(v.0.5.1), RColorBrewer(v.1.1-2), httr(v.1.4.1), GenomeInfoDb(v.1.22.0), tools(v.3.6.1), backports(v.1.1.5), R6(v.2.4.1), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.6.1), rvest(v.0.3.5), Biobase(v.2.46.0), Cairo(v.1.5-10), flashClust(v.1.01-2), xml2(v.1.2.2), DelayedArray(v.0.12.0), plotly(v.4.9.1), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.22), Rsamtools(v.2.2.1), rmarkdown(v.1.17), XVector(v.0.26.0), pkgconfig(v.2.0.3), htmltools(v.0.4.0), fastmap(v.1.0.1), FactoMineR(v.1.42), highr(v.0.8), htmlwidgets(v.1.5.1), rlang(v.0.4.1), rstudioapi(v.0.10), shiny(v.1.4.0), farver(v.2.0.1), zoo(v.1.8-6), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.20.0), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.2), leaps(v.3.0), Matrix(v.1.2-17), Rcpp(v.1.0.3), munsell(v.0.5.0), S4Vectors(v.0.24.0), lifecycle(v.0.1.0), scatterplot3d(v.0.3-41), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.4), SummarizedExperiment(v.1.16.0), zlibbioc(v.1.32.0), plyr(v.1.8.4), grid(v.3.6.1), promises(v.1.1.0), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.54.0), hms(v.0.5.2), zeallot(v.0.1.0), knitr(v.1.26), pillar(v.1.4.2), GenomicRanges(v.1.38.0), reshape2(v.1.4.3), stats4(v.3.6.1), glue(v.1.3.1), packrat(v.0.5.0), evaluate(v.0.14), ShortRead(v.1.44.0), latticeExtra(v.0.6-28), data.table(v.1.12.6), httpuv(v.1.5.2), vctrs(v.0.2.0), gtable(v.0.3.0), purrr(v.0.3.3), tidyr(v.1.0.0), assertthat(v.0.2.1), xfun(v.0.11), mime(v.0.7), xtable(v.1.8-4), later(v.1.0.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.0), cluster(v.2.1.0) and ellipsis(v.0.3.0)